Data is available on Synapse.
Summary
This includes code and plots for the final version of the paper. Exploratory analysis and intermediate processing steps are too extensive to be included here
Sendai Expression

Biotype of expressed genes
|
Biotype
|
Count
|
|
protein_coding
|
11681
|
|
processed_transcript
|
1691
|
|
antisense
|
1488
|
|
lincRNA
|
879
|
|
processed_pseudogene
|
822
|
|
nonsense_mediated_decay
|
708
|
|
retained_intron
|
671
|
|
sense_intronic
|
197
|
|
unprocessed_pseudogene
|
163
|
|
sense_overlapping
|
93
|
|
miRNA
|
66
|
|
misc_RNA
|
58
|
|
snoRNA
|
56
|
|
transcribed_unprocessed_pseudogene
|
47
|
|
pseudogene
|
37
|
|
transcribed_processed_pseudogene
|
28
|
|
snRNA
|
27
|
|
unitary_pseudogene
|
16
|
|
3prime_overlapping_ncrna
|
12
|
|
rRNA
|
8
|
|
Mt_tRNA
|
4
|
|
polymorphic_pseudogene
|
4
|
|
non_stop_decay
|
3
|
|
IG_V_pseudogene
|
1
|
|
TR_C_gene
|
1
|
Check sex on 94 samples

| USP9Y |
| UTY |
| NLGN4Y |
| ZFY |
| RPS4Y1 |
| TXLNG2P |
Detect sample contamination with VerifyBamID
The labeling of Donor 499 was corrected manually 
Excluded due to sample mislabeling, contamination or issues with expression on the sex chromosomes
|
Sample.Name
|
|
1275-B-3F
|
|
1275-B-3N
|
|
1275-C-1F
|
|
1275-C-1N
|
|
2476-1-4F
|
|
2476-1-4N
|
|
2484-2aF
|
|
2484-2aN
|
|
3113-3-21F
|
|
3113-3-21N
|
|
3121-2-1F
|
|
3121-2-1N
|
|
3121-2-MSSM2F
|
|
3121-2-MSSM2N
|
|
3130-2-1F
|
|
3130-2-1N
|
|
676-1-2N
|
Samples included in analysis
|
|
6_wk_FB_neuron
|
NPC
|
|
CT
|
20
|
20
|
|
SZ
|
19
|
18
|
QC metrics

Check sex on cleaned dataset

Differential gene expression based on Sendai virus exression
[1] “DE genes at FDR < 5%: 2738”
Yaminaka factors
POU5F1 is not expressed at a sufficient level
| ENSG00000136997 |
0.3021708 |
3.1929949 |
2.1221004 |
0.0371472 |
0.0865717 |
MYC |
| ENSG00000181449 |
-0.0561620 |
8.7614381 |
-1.0330145 |
0.3049324 |
0.2868959 |
SOX2 |
| ENSG00000136826 |
-0.1388002 |
0.0752657 |
-0.8533798 |
0.3961789 |
0.3310979 |
KLF4 |


Compare Neurons and NPC


Enrichments for genes up in Neurons
|
Gene Set
|
Gene Set Size
|
Expected Hits
|
Observed Hits
|
OR
|
Pvalue
|
|
tissue_exp_brain
|
495.00
|
65.97
|
241
|
3.65
|
9.20E-84
|
|
c2.BENPORATH_ES_WITH_H3K27ME3
|
730.00
|
97.29
|
283
|
2.91
|
2.29E-70
|
|
c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3
|
347.00
|
46.25
|
162
|
3.50
|
7.81E-53
|
|
c2.BENPORATH_SUZ12_TARGETS
|
664.00
|
88.50
|
240
|
2.71
|
9.40E-53
|
|
c2.BENPORATH_EED_TARGETS
|
705.00
|
93.96
|
240
|
2.55
|
2.13E-47
|
|
c2.BENPORATH_PRC2_TARGETS
|
391.00
|
52.11
|
163
|
3.13
|
5.01E-45
|
|
c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP
|
1225.00
|
163.27
|
340
|
2.08
|
1.26E-44
|
|
c2.MIKKELSEN_MCV6_HCP_WITH_H3K27ME3
|
285.00
|
37.98
|
129
|
3.40
|
2.42E-40
|
|
c2.MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3
|
215.00
|
28.65
|
108
|
3.77
|
3.83E-39
|
|
c5.GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMBRANE
|
998.00
|
133.01
|
282
|
2.12
|
3.13E-38
|
|
c5.GO_CELL_CELL_SIGNALING
|
502.00
|
66.91
|
173
|
2.59
|
7.35E-35
|
|
c5.GO_NEURON_PART
|
1088.00
|
145.01
|
282
|
1.94
|
5.04E-31
|
|
c2.MIKKELSEN_NPC_HCP_WITH_H3K27ME3
|
192.00
|
25.59
|
90
|
3.52
|
7.31E-30
|
|
c2.NABA_MATRISOME
|
555.00
|
73.97
|
174
|
2.35
|
2.58E-29
|
|
c5.GO_SYNAPSE
|
677.00
|
90.23
|
198
|
2.19
|
7.62E-29
|
|
c5.GO_SYNAPTIC_SIGNALING
|
331.00
|
44.11
|
123
|
2.79
|
1.94E-28
|
|
c2.ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY
|
873.00
|
116.35
|
235
|
2.02
|
2.55E-28
|
|
c2.SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN
|
223.00
|
29.72
|
96
|
3.23
|
3.72E-28
|
|
tissue_exp_testis
|
452.00
|
60.24
|
149
|
2.47
|
9.65E-28
|
|
c5.GO_METAL_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY
|
298.00
|
39.72
|
112
|
2.82
|
1.80E-26
|

Enrichments for genes up in NPCs
|
Gene Set
|
Gene Set Size
|
Expected Hits
|
Observed Hits
|
OR
|
Pvalue
|
|
c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP
|
547
|
33.21
|
260
|
7.83
|
4.96E-176
|
|
c2.DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP
|
304
|
18.46
|
190
|
10.29
|
1.04E-156
|
|
c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED
|
690
|
41.89
|
247
|
5.90
|
7.73E-131
|
|
c2.KOBAYASHI_EGFR_SIGNALING_24HR_DN
|
236
|
14.33
|
153
|
10.68
|
6.86E-129
|
|
c4.MODULE_54
|
241
|
14.63
|
150
|
10.25
|
2.58E-122
|
|
c2.ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER
|
137
|
8.32
|
111
|
13.34
|
2.69E-111
|
|
c7.GSE15750_DAY6_VS_DAY10_TRAF6KO_EFF_CD8_TCELL_UP
|
186
|
11.29
|
122
|
10.80
|
3.20E-103
|
|
c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP
|
1176
|
71.40
|
282
|
3.95
|
6.11E-101
|
|
c2.SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6
|
416
|
25.26
|
170
|
6.73
|
6.49E-99
|
|
c7.GSE15750_DAY6_VS_DAY10_EFF_CD8_TCELL_UP
|
189
|
11.48
|
119
|
10.37
|
1.86E-97
|
|
c5.GO_CHROMOSOME
|
778
|
47.24
|
226
|
4.78
|
2.87E-97
|
|
c2.CHANG_CYCLING_GENES
|
145
|
8.80
|
103
|
11.70
|
1.19E-92
|
|
c5.GO_CHROMOSOME_ORGANIZATION
|
875
|
53.13
|
233
|
4.39
|
8.60E-92
|
|
c2.SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP
|
147
|
8.93
|
102
|
11.43
|
4.80E-90
|
|
c2.ZHANG_TLX_TARGETS_60HR_DN
|
263
|
15.97
|
131
|
8.20
|
3.32E-89
|
|
c2.REACTOME_CELL_CYCLE
|
384
|
23.31
|
155
|
6.65
|
6.43E-89
|
|
h.HALLMARK_E2F_TARGETS
|
199
|
12.08
|
115
|
9.52
|
5.45E-88
|
|
c2.PUJANA_BRCA2_PCC_NETWORK
|
388
|
23.56
|
153
|
6.49
|
5.80E-86
|
|
c7.GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_12H_UP
|
171
|
10.38
|
105
|
10.11
|
3.42E-84
|
|
c2.WHITEFORD_PEDIATRIC_CANCER_MARKERS
|
110
|
6.68
|
86
|
12.88
|
1.49E-83
|

Overlap between NPC and neuron
##
## Attaching package: 'sets'
## The following object is masked from 'package:igraph':
##
## %>%
## The following object is masked from 'package:synapseClient':
##
## set
## [1] "cutoff: log2 RPKM > 0"

## [1] "cutoff: log2 RPKM > 1"

## [1] "cutoff: log2 RPKM > 2"

## [1] "cutoff: log2 RPKM > 3"

## [1] "cutoff: log2 RPKM > 4"

## [1] "cutoff: log2 RPKM > 5"

## [1] "cutoff: log2 RPKM > 6"


Cibersort results
Histogram of cell type composition: all samples

There is no case-control difference in cell type scores


Cell composition in Neurons and NPC

Differential expression based on cell fraction
Enrichment test for gene positively correlated with cell fraction
6_wk_FB_neuron-Astrocytes
| CMC-modules_peru |
114 |
67 |
108 |
1.6 |
2.5e-18 |
| CMC-modules_lightgreen |
199 |
118 |
173 |
1.5 |
6.0e-18 |
| c4.MODULE_1 |
318 |
188 |
253 |
1.3 |
4.5e-15 |
| c2.LEE_BMP2_TARGETS_UP |
598 |
354 |
442 |
1.2 |
1.0e-14 |
| c2.MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H |
826 |
488 |
584 |
1.2 |
9.7e-13 |
| c4.MODULE_47 |
196 |
116 |
162 |
1.4 |
1.0e-12 |
| c5.GO_EXTRACELLULAR_STRUCTURE_ORGANIZATI |
220 |
130 |
179 |
1.4 |
1.1e-12 |
| h.HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSI |
177 |
105 |
148 |
1.4 |
1.5e-12 |
| c4.MODULE_2 |
328 |
194 |
252 |
1.3 |
7.0e-12 |
| c2.BOQUEST_STEM_CELL_UP |
207 |
122 |
168 |
1.4 |
8.3e-12 |
6_wk_FB_neuron-Neuron
| tissue_exp_brain |
495 |
340 |
438 |
1.3 |
5.2e-26 |
| CMC-modules_red |
689 |
473 |
566 |
1.2 |
1.6e-16 |
| CMC-modules_blue |
1154 |
792 |
904 |
1.1 |
1.7e-14 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
238 |
294 |
1.2 |
2.7e-12 |
| c5.GO_SYNAPTIC_SIGNALING |
331 |
227 |
278 |
1.2 |
8.4e-11 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
113 |
146 |
1.3 |
1.6e-09 |
| c5.GO_CELL_CELL_SIGNALING |
502 |
344 |
403 |
1.2 |
1.8e-09 |
| secondary_FMRP-targets |
770 |
528 |
600 |
1.1 |
2.7e-09 |
| abnormal_synaptic_transmission |
386 |
265 |
315 |
1.2 |
4.0e-09 |
| c5.GO_SYNAPSE |
677 |
465 |
531 |
1.1 |
4.2e-09 |
6_wk_FB_neuron-Oligodendrocyte_Precursor_Cell
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
779 |
920 |
1.2 |
2.8e-19 |
| CMC-modules_peru |
114 |
73 |
108 |
1.5 |
3.5e-15 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
348 |
430 |
1.2 |
9.0e-15 |
| c2.MILI_PSEUDOPODIA_HAPTOTAXIS_DN |
626 |
398 |
483 |
1.2 |
7.6e-14 |
| c5.GO_PROTEIN_COMPLEX_SUBUNIT_ORGANIZATI |
1299 |
826 |
947 |
1.1 |
8.1e-14 |
| c2.SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN |
223 |
142 |
189 |
1.3 |
1.6e-12 |
| c2.LU_AGING_BRAIN_UP |
239 |
152 |
199 |
1.3 |
1.3e-11 |
| c5.GO_ENDOPLASMIC_RETICULUM |
1285 |
818 |
924 |
1.1 |
3.4e-11 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANC |
397 |
253 |
312 |
1.2 |
4.8e-11 |
| c5.GO_ENDOPLASMIC_RETICULUM_PART |
926 |
589 |
679 |
1.2 |
6.4e-11 |
6_wk_FB_neuron-Fibroblast
| c2.REN_ALVEOLAR_RHABDOMYOSARCOMA_DN |
391 |
278 |
352 |
1.3 |
3.1e-20 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
871 |
992 |
1.1 |
9.7e-17 |
| CMC-modules_lightcyan |
268 |
191 |
243 |
1.3 |
2.8e-15 |
| c2.BLALOCK_ALZHEIMERS_DISEASE_UP |
1486 |
1056 |
1180 |
1.1 |
1.1e-14 |
| c5.GO_ENDOPLASMIC_RETICULUM |
1285 |
913 |
1027 |
1.1 |
3.2e-14 |
| c5.GO_ENDOPLASMIC_RETICULUM_PART |
926 |
658 |
752 |
1.1 |
2.1e-13 |
| c4.MODULE_1 |
318 |
226 |
278 |
1.2 |
2.0e-12 |
| c4.MODULE_47 |
196 |
139 |
178 |
1.3 |
1.1e-11 |
| c5.GO_MOVEMENT_OF_CELL_OR_SUBCELLULAR_CO |
951 |
676 |
764 |
1.1 |
1.1e-11 |
| c5.GO_LOCOMOTION |
785 |
558 |
634 |
1.1 |
1.2e-10 |
6_wk_FB_neuron-MEF
| c5.GO_POLY_A_RNA_BINDING |
1113 |
805 |
970 |
1.2 |
4.9e-35 |
| c5.GO_RNA_BINDING |
1466 |
1060 |
1239 |
1.2 |
3.8e-31 |
| c5.GO_RIBONUCLEOPROTEIN_COMPLEX |
660 |
477 |
595 |
1.2 |
9.9e-31 |
| c4.MODULE_83 |
308 |
223 |
297 |
1.3 |
2.3e-29 |
| pli_MID |
2881 |
2083 |
2308 |
1.1 |
9.3e-27 |
| c2.HSIAO_HOUSEKEEPING_GENES |
374 |
270 |
350 |
1.3 |
3.6e-26 |
| c4.MODULE_114 |
319 |
231 |
301 |
1.3 |
2.1e-24 |
| c5.GO_RIBONUCLEOPROTEIN_COMPLEX_BIOGENES |
419 |
303 |
384 |
1.3 |
1.4e-23 |
| c4.MODULE_151 |
298 |
215 |
281 |
1.3 |
1.0e-22 |
| c5.GO_RNA_PROCESSING |
781 |
565 |
674 |
1.2 |
7.1e-22 |
6_wk_FB_neuron-Myocyte
| c5.GO_RNA_BINDING |
1466 |
994 |
1240 |
1.2 |
6.7e-53 |
| c5.GO_POLY_A_RNA_BINDING |
1113 |
755 |
963 |
1.3 |
4.7e-50 |
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
1001 |
1214 |
1.2 |
3.9e-39 |
| c5.GO_RIBONUCLEOPROTEIN_COMPLEX |
660 |
448 |
587 |
1.3 |
2.2e-38 |
| CMC-modules_brown |
897 |
608 |
766 |
1.3 |
2.7e-35 |
| c4.MODULE_83 |
308 |
209 |
295 |
1.4 |
7.7e-35 |
| c5.GO_RNA_PROCESSING |
781 |
530 |
674 |
1.3 |
4.0e-34 |
| c4.MORF_UBE2I |
236 |
160 |
231 |
1.4 |
1.2e-32 |
| c4.MODULE_114 |
319 |
216 |
302 |
1.4 |
1.4e-32 |
| c4.MORF_CSNK2B |
286 |
194 |
274 |
1.4 |
1.7e-32 |
6_wk_FB_neuron-hiPSC
| c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED |
690 |
347 |
507 |
1.5 |
5.6e-37 |
| c2.MANALO_HYPOXIA_DN |
279 |
140 |
240 |
1.7 |
8.6e-37 |
| c5.GO_CHROMOSOME_ORGANIZATION |
875 |
440 |
613 |
1.4 |
2.8e-34 |
| c2.PUJANA_CHEK2_PCC_NETWORK |
730 |
367 |
522 |
1.4 |
7.6e-33 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
275 |
404 |
1.5 |
2.3e-30 |
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
743 |
949 |
1.3 |
4.3e-30 |
| c5.GO_CHROMOSOME |
778 |
391 |
543 |
1.4 |
1.0e-29 |
| c2.DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP |
304 |
153 |
244 |
1.6 |
9.5e-28 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_DN |
1224 |
616 |
797 |
1.3 |
1.1e-27 |
| c2.LEE_BMP2_TARGETS_DN |
826 |
416 |
564 |
1.4 |
5.3e-27 |
NPC-Astrocytes
| tissue_exp_brain |
495 |
320 |
401 |
1.3 |
4.0e-16 |
| secondary_FMRP-targets |
770 |
498 |
597 |
1.2 |
1.6e-15 |
| c5.GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMB |
998 |
645 |
730 |
1.1 |
2.2e-09 |
| c5.GO_NEURON_PART |
1088 |
704 |
790 |
1.1 |
4.5e-09 |
| c5.GO_REGULATION_OF_NEUROTRANSMITTER_LEV |
165 |
107 |
140 |
1.3 |
5.2e-09 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
1000 |
647 |
728 |
1.1 |
9.2e-09 |
| c5.GO_SYNAPTIC_SIGNALING |
331 |
214 |
261 |
1.2 |
1.0e-08 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
792 |
881 |
1.1 |
1.2e-08 |
| c2.BENPORATH_ES_WITH_H3K27ME3 |
730 |
472 |
541 |
1.1 |
1.4e-08 |
| c4.MODULE_66 |
474 |
307 |
361 |
1.2 |
3.0e-08 |
NPC-Neuron
| tissue_exp_brain |
495 |
279 |
399 |
1.4 |
5.7e-31 |
| c2.BENPORATH_ES_WITH_H3K27ME3 |
730 |
411 |
507 |
1.2 |
7.0e-14 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANC |
397 |
224 |
294 |
1.3 |
1.0e-13 |
| secondary_FMRP-targets |
770 |
434 |
528 |
1.2 |
7.1e-13 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
93 |
136 |
1.5 |
8.6e-13 |
| c2.BENPORATH_SUZ12_TARGETS |
664 |
374 |
455 |
1.2 |
3.5e-11 |
| CMC-modules_blue |
1154 |
650 |
754 |
1.2 |
6.4e-11 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
196 |
253 |
1.3 |
8.5e-11 |
| CMC-modules_red |
689 |
388 |
468 |
1.2 |
1.3e-10 |
| c5.GO_NEURON_PART |
1088 |
613 |
711 |
1.2 |
2.2e-10 |
NPC-Oligodendrocyte_Precursor_Cell
| secondary_FMRP-targets |
770 |
498 |
586 |
1.2 |
1.5e-12 |
| c5.GO_CELL_PROJECTION |
1508 |
975 |
1088 |
1.1 |
4.7e-11 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
1000 |
647 |
733 |
1.1 |
1.0e-09 |
| c5.GO_NEURON_PROJECTION |
835 |
540 |
614 |
1.1 |
1.1e-08 |
| c5.GO_VACUOLE |
959 |
620 |
699 |
1.1 |
1.3e-08 |
| c5.GO_GOLGI_APPARATUS |
1210 |
782 |
864 |
1.1 |
1.3e-07 |
| c5.GO_NEURON_PART |
1088 |
703 |
781 |
1.1 |
1.4e-07 |
| c2.BERENJENO_TRANSFORMED_BY_RHOA_DN |
365 |
236 |
281 |
1.2 |
1.8e-07 |
| primary_PSD_(human_core) |
644 |
416 |
476 |
1.1 |
1.8e-07 |
| c5.GO_VACUOLAR_PART |
577 |
373 |
429 |
1.1 |
2.4e-07 |
NPC-Newly_Formed_Oligodendrocyte
| tissue_exp_brain |
495 |
285 |
415 |
1.5 |
2.9e-37 |
| c2.BENPORATH_ES_WITH_H3K27ME3 |
730 |
420 |
557 |
1.3 |
1.3e-27 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
200 |
283 |
1.4 |
5.6e-22 |
| c2.BENPORATH_SUZ12_TARGETS |
664 |
382 |
494 |
1.3 |
1.7e-20 |
| c2.MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 |
285 |
164 |
235 |
1.4 |
1.2e-19 |
| c2.BENPORATH_PRC2_TARGETS |
391 |
225 |
306 |
1.4 |
2.0e-18 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANC |
397 |
228 |
308 |
1.3 |
1.5e-17 |
| tissue_exp_testis |
452 |
260 |
342 |
1.3 |
2.3e-16 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
704 |
837 |
1.2 |
3.7e-16 |
| c5.GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMB |
998 |
574 |
687 |
1.2 |
1.9e-14 |
NPC-Fibroblast
| c2.NABA_MATRISOME |
555 |
306 |
397 |
1.3 |
6.3e-16 |
| c2.WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216 |
297 |
164 |
230 |
1.4 |
6.6e-16 |
| Peptide_chain_elongation |
82 |
45 |
77 |
1.7 |
6.3e-15 |
| c2.REACTOME_PEPTIDE_CHAIN_ELONGATION |
84 |
46 |
78 |
1.7 |
2.3e-14 |
| Eukaryotic_Translation_Elongation |
84 |
46 |
78 |
1.7 |
2.3e-14 |
| Formation_of_a_pool_of_free_40S_subunit |
92 |
51 |
84 |
1.7 |
3.1e-14 |
| Viral_mRNA_Translation |
83 |
46 |
77 |
1.7 |
4.0e-14 |
| viral transcription |
82 |
45 |
76 |
1.7 |
6.7e-14 |
| c2.LEE_BMP2_TARGETS_UP |
598 |
330 |
417 |
1.3 |
8.4e-14 |
| 3’_-UTR-mediated_translational_regulati |
102 |
56 |
90 |
1.6 |
5.4e-13 |
NPC-MEF
| c4.MORF_RAD23A |
343 |
240 |
319 |
1.3 |
1.3e-26 |
| c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED |
690 |
482 |
598 |
1.2 |
2.8e-26 |
| c4.MORF_BUB3 |
275 |
192 |
261 |
1.4 |
6.6e-26 |
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
1031 |
1194 |
1.2 |
3.3e-24 |
| c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_U |
1176 |
821 |
966 |
1.2 |
1.0e-23 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
382 |
479 |
1.3 |
2.2e-23 |
| c4.MORF_CSNK2B |
286 |
200 |
266 |
1.3 |
2.2e-22 |
| c2.DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP |
1312 |
916 |
1059 |
1.2 |
7.7e-21 |
| c2.SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_U |
147 |
103 |
145 |
1.4 |
1.9e-20 |
| c5.GO_CELL_CYCLE |
1180 |
824 |
957 |
1.2 |
4.6e-20 |
NPC-Myocyte
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
754 |
1005 |
1.3 |
3.9e-44 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_DN |
1224 |
625 |
854 |
1.4 |
1.2e-43 |
| c2.PUJANA_CHEK2_PCC_NETWORK |
730 |
373 |
546 |
1.5 |
2.9e-41 |
| CMC-modules_black |
625 |
319 |
474 |
1.5 |
1.6e-38 |
| c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_U |
1176 |
600 |
810 |
1.3 |
4.7e-38 |
| c2.CAIRO_HEPATOBLASTOMA_CLASSES_UP |
581 |
297 |
434 |
1.5 |
1.2e-32 |
| c2.JOHNSTONE_PARVB_TARGETS_3_DN |
862 |
440 |
598 |
1.4 |
2.5e-29 |
| c2.RODRIGUES_THYROID_CARCINOMA_POORLY_DI |
604 |
308 |
440 |
1.4 |
6.5e-29 |
| c2.LEE_BMP2_TARGETS_DN |
826 |
422 |
575 |
1.4 |
7.9e-29 |
| c4.GNF2_EIF3S6 |
118 |
60 |
114 |
1.9 |
1.6e-28 |
NPC-hiPSC
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
852 |
1123 |
1.3 |
3.6e-54 |
| c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_U |
1176 |
679 |
913 |
1.3 |
2.7e-50 |
| c2.PUJANA_CHEK2_PCC_NETWORK |
730 |
421 |
593 |
1.4 |
1.8e-43 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
316 |
460 |
1.5 |
1.9e-41 |
| c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED |
690 |
398 |
559 |
1.4 |
2.6e-40 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_DN |
1224 |
706 |
914 |
1.3 |
5.5e-38 |
| c2.PUJANA_BRCA2_PCC_NETWORK |
388 |
224 |
337 |
1.5 |
1.5e-36 |
| c2.CAIRO_HEPATOBLASTOMA_CLASSES_UP |
581 |
335 |
473 |
1.4 |
3.4e-35 |
| Cell_Cycle |
455 |
263 |
382 |
1.5 |
3.4e-34 |
| h.HALLMARK_E2F_TARGETS |
199 |
115 |
188 |
1.6 |
1.9e-32 |
Analysis of original data



Analysis after correcting for cell type composition scores for fibroblasts and MEF



Color PCA by CTC score

Fit linear model to test difference in CTC scores between cell types



Correlation of CTC scores with principal components

## Projected run time: ~ 20 min
## Projected run time: ~ 1 min
## [1] 0.02234939
## [1] 0.02350184
## [1] 0.003482901
##
## Wilcoxon signed rank test with continuity correction
##
## data: vpCellFrac2$Donor and vpCellFrac_minimal$Donor
## V = 39876000, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
all cell fractions

accounting for MEF and Fibroblast increases donor contributions
## Projected run time: ~ 1 min
## Projected run time: ~ 1 min
##
## Paired t-test
##
## data: df$adjusted and df$original
## t = 15.712, df = 18909, p-value < 2.2e-16
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 0.003048411 0.003917390
## sample estimates:
## mean of the differences
## 0.003482901
Percent bars

VariancePartition within each cell type

Compare donor effect

variancePartition: include technical variables
## Projected run time: ~ 5 min

Correlation between covariates

Differential expression between cases and controls in combined NPC + neuron dataset
Volcano plot

Genes with FDR < 30%
| ENSG00000230847 |
-3.8867431 |
-2.0458924 |
-7.503823 |
0.0000000 |
0.0000020 |
ENSG00000230847 |
| ENSG00000164930 |
-0.7773348 |
4.8643554 |
-5.911893 |
0.0000001 |
0.0008782 |
FZD6 |
| ENSG00000226259 |
-1.1458273 |
2.3980778 |
-5.496058 |
0.0000005 |
0.0031800 |
GTF2H2B |
| ENSG00000236725 |
-1.0340737 |
0.4658067 |
-5.316601 |
0.0000011 |
0.0039572 |
ENSG00000236725 |
| ENSG00000269337 |
-1.0984407 |
0.7260166 |
-5.313372 |
0.0000011 |
0.0039572 |
ENSG00000269337 |
| ENSG00000169629 |
-0.9328454 |
2.8967989 |
-4.990793 |
0.0000039 |
0.0116728 |
RGPD8 |
| ENSG00000184988 |
-0.6371885 |
0.6108187 |
-4.752049 |
0.0000097 |
0.0199287 |
TMEM106A |
| ENSG00000177873 |
-0.4751565 |
3.6251045 |
-4.744838 |
0.0000100 |
0.0199287 |
ZNF619 |
| ENSG00000145246 |
0.8099405 |
3.4869808 |
4.737294 |
0.0000103 |
0.0199287 |
ATP10D |
| ENSG00000121691 |
1.5711365 |
4.3941262 |
4.717053 |
0.0000111 |
0.0199287 |
CAT |
| ENSG00000003402 |
-1.2184673 |
2.9784138 |
-4.658510 |
0.0000138 |
0.0225783 |
CFLAR |
| ENSG00000173894 |
0.3974699 |
5.3493957 |
4.539741 |
0.0000215 |
0.0322191 |
CBX2 |
| ENSG00000237945 |
-1.4449894 |
3.0295611 |
-4.474223 |
0.0000273 |
0.0378749 |
LINC00649 |
| ENSG00000037757 |
-1.0264047 |
3.0641913 |
-4.421709 |
0.0000332 |
0.0403826 |
MRI1 |
| ENSG00000115828 |
-1.4442631 |
0.6431161 |
-4.417693 |
0.0000336 |
0.0403826 |
QPCT |
| ENSG00000181234 |
3.9832515 |
-0.9565400 |
4.375613 |
0.0000392 |
0.0441347 |
TMEM132C |
| ENSG00000164669 |
-0.9330823 |
-0.2461149 |
-4.356789 |
0.0000420 |
0.0444782 |
INTS4L1 |
| ENSG00000240342 |
-0.6669021 |
4.8380931 |
-4.336412 |
0.0000452 |
0.0452268 |
RPS2P5 |
| ENSG00000229404 |
-1.7586482 |
-0.9581430 |
-4.311301 |
0.0000495 |
0.0466317 |
LINC00858 |
| ENSG00000254353 |
-2.1384802 |
-0.4100724 |
-4.291721 |
0.0000531 |
0.0466317 |
ENSG00000254353 |
| ENSG00000226002 |
0.5981007 |
0.1750937 |
4.285220 |
0.0000544 |
0.0466317 |
ENSG00000226002 |
| ENSG00000244026 |
-0.5236215 |
3.8687373 |
-4.177683 |
0.0000799 |
0.0653742 |
FAM86DP |
| ENSG00000185985 |
2.7724325 |
5.1279631 |
4.162363 |
0.0000843 |
0.0660238 |
SLITRK2 |
| ENSG00000236383 |
-0.6271087 |
-0.4722674 |
-4.146970 |
0.0000891 |
0.0668164 |
LINC00854 |
| ENSG00000229789 |
-1.2992945 |
-0.2195011 |
-4.131695 |
0.0000940 |
0.0677005 |
ENSG00000229789 |
| ENSG00000010704 |
-0.9534242 |
-0.6692788 |
-4.104042 |
0.0001036 |
0.0709274 |
HFE |
| ENSG00000228463 |
-1.3430626 |
-0.4915192 |
-4.096619 |
0.0001064 |
0.0709274 |
ENSG00000228463 |
| ENSG00000115507 |
1.9964444 |
-0.0009156 |
4.075118 |
0.0001147 |
0.0725178 |
OTX1 |
| ENSG00000239959 |
-0.7577011 |
-0.1855192 |
-4.069923 |
0.0001168 |
0.0725178 |
ENPP7P2 |
| ENSG00000162618 |
-1.6783969 |
-0.7365519 |
-4.043841 |
0.0001279 |
0.0733200 |
ELTD1 |
| ENSG00000198715 |
-0.6225848 |
2.0519971 |
-4.037013 |
0.0001310 |
0.0733200 |
C1orf85 |
| ENSG00000107829 |
-0.5636433 |
1.8306642 |
-4.028719 |
0.0001349 |
0.0733200 |
FBXW4 |
| ENSG00000196569 |
-1.2655757 |
3.3493015 |
-4.027240 |
0.0001356 |
0.0733200 |
LAMA2 |
| ENSG00000221870 |
2.5063090 |
1.4534521 |
4.021192 |
0.0001385 |
0.0733200 |
TMEM257 |
| ENSG00000227775 |
0.4286190 |
4.0581385 |
3.993127 |
0.0001526 |
0.0785141 |
ENSG00000227775 |
| ENSG00000160789 |
-0.3087472 |
6.1850559 |
-3.945999 |
0.0001796 |
0.0886165 |
LMNA |
| ENSG00000212719 |
-2.8235614 |
2.0022500 |
-3.938600 |
0.0001842 |
0.0886165 |
C17orf51 |
| ENSG00000259085 |
0.4518444 |
0.8237710 |
3.934224 |
0.0001870 |
0.0886165 |
ENSG00000259085 |
| ENSG00000137962 |
-0.8405123 |
5.9505584 |
-3.925476 |
0.0001927 |
0.0889780 |
ARHGAP29 |
| ENSG00000148942 |
-1.7992311 |
-0.7765750 |
-3.905677 |
0.0002063 |
0.0928457 |
SLC5A12 |
| ENSG00000234431 |
-1.1610396 |
-0.0453674 |
-3.836649 |
0.0002609 |
0.1145893 |
ENSG00000234431 |
| ENSG00000106868 |
-0.4221252 |
5.3831940 |
-3.801357 |
0.0002940 |
0.1260332 |
SUSD1 |
| ENSG00000256043 |
-1.1396397 |
2.1885944 |
-3.734748 |
0.0003676 |
0.1484549 |
CTSO |
| ENSG00000183036 |
1.0568761 |
0.2824591 |
3.731252 |
0.0003719 |
0.1484549 |
PCP4 |
| ENSG00000255983 |
-1.7770246 |
-1.6255799 |
-3.724899 |
0.0003799 |
0.1484549 |
ENSG00000255983 |
| ENSG00000108946 |
-0.1539076 |
8.5710566 |
-3.720296 |
0.0003857 |
0.1484549 |
PRKAR1A |
| ENSG00000118946 |
-0.6964719 |
6.9945080 |
-3.710494 |
0.0003985 |
0.1484549 |
PCDH17 |
| ENSG00000146833 |
-1.7925956 |
2.0933749 |
-3.708006 |
0.0004018 |
0.1484549 |
TRIM4 |
| ENSG00000238286 |
0.3957608 |
0.6291523 |
3.706382 |
0.0004040 |
0.1484549 |
SLC35E1P1 |
| ENSG00000234719 |
-0.9946496 |
0.9947928 |
-3.679553 |
0.0004416 |
0.1590205 |
ENSG00000234719 |
| ENSG00000222489 |
0.4179907 |
0.2003903 |
3.668398 |
0.0004582 |
0.1594946 |
ENSG00000222489 |
| ENSG00000145736 |
-0.5293506 |
3.2139470 |
-3.666787 |
0.0004606 |
0.1594946 |
GTF2H2 |
| ENSG00000234171 |
-0.3666779 |
2.5715243 |
-3.646265 |
0.0004929 |
0.1674384 |
ENSG00000234171 |
| ENSG00000263535 |
-0.5471106 |
0.2504930 |
-3.637930 |
0.0005066 |
0.1676472 |
AK4P1 |
| ENSG00000105963 |
-0.5320618 |
0.9723243 |
-3.629585 |
0.0005206 |
0.1676472 |
ADAP1 |
| ENSG00000185518 |
-1.4407644 |
-0.7248376 |
-3.629134 |
0.0005214 |
0.1676472 |
SV2B |
| ENSG00000136104 |
0.3501590 |
3.8369805 |
3.609525 |
0.0005560 |
0.1715273 |
RNASEH2B |
| ENSG00000232300 |
0.5848956 |
-0.3102700 |
3.597250 |
0.0005788 |
0.1715273 |
FAM215B |
| ENSG00000266937 |
-0.2438614 |
1.6488055 |
-3.592392 |
0.0005880 |
0.1715273 |
ENSG00000266937 |
| ENSG00000198932 |
-0.5232759 |
4.2805161 |
-3.590830 |
0.0005910 |
0.1715273 |
GPRASP1 |
| ENSG00000105971 |
-0.4935931 |
4.8915284 |
-3.586868 |
0.0005987 |
0.1715273 |
CAV2 |
| ENSG00000066382 |
1.6313657 |
3.2008651 |
3.586588 |
0.0005993 |
0.1715273 |
MPPED2 |
| ENSG00000169436 |
2.9415822 |
-1.3911095 |
3.586128 |
0.0006002 |
0.1715273 |
COL22A1 |
| ENSG00000022556 |
2.4000333 |
1.2777887 |
3.576075 |
0.0006201 |
0.1744663 |
NLRP2 |
| ENSG00000227318 |
-1.7281778 |
-0.6086402 |
-3.568752 |
0.0006351 |
0.1751623 |
ENSG00000227318 |
| ENSG00000170089 |
-0.4997211 |
2.3869475 |
-3.565386 |
0.0006421 |
0.1751623 |
ENSG00000170089 |
| ENSG00000196993 |
-0.7658407 |
0.0667859 |
-3.556916 |
0.0006600 |
0.1773572 |
NPIPB9 |
| ENSG00000217512 |
0.3593747 |
0.6649783 |
3.523761 |
0.0007347 |
0.1945323 |
ENSG00000217512 |
| ENSG00000036448 |
0.7667332 |
1.7145378 |
3.512307 |
0.0007623 |
0.1953258 |
MYOM2 |
| ENSG00000141837 |
-1.0014302 |
1.3880998 |
-3.507836 |
0.0007733 |
0.1953258 |
CACNA1A |
| ENSG00000269600 |
1.6893815 |
-1.3032529 |
3.507404 |
0.0007744 |
0.1953258 |
ENSG00000269600 |
| ENSG00000169955 |
-0.6639366 |
1.6450844 |
-3.504748 |
0.0007811 |
0.1953258 |
ZNF747 |
| ENSG00000176978 |
-0.4750891 |
3.9911880 |
-3.496565 |
0.0008019 |
0.1977826 |
DPP7 |
| ENSG00000146707 |
-0.3052560 |
3.3309046 |
-3.484563 |
0.0008333 |
0.2027673 |
POMZP3 |
| ENSG00000126822 |
0.9815936 |
4.3171322 |
3.470810 |
0.0008708 |
0.2090667 |
PLEKHG3 |
| ENSG00000253954 |
0.8588332 |
-0.0100037 |
3.449438 |
0.0009323 |
0.2196709 |
HMGN1P38 |
| ENSG00000011405 |
0.1496642 |
7.6232380 |
3.447050 |
0.0009394 |
0.2196709 |
PIK3C2A |
| ENSG00000105136 |
-0.1753927 |
4.7028745 |
-3.438130 |
0.0009665 |
0.2230963 |
ZNF419 |
| ENSG00000128591 |
-0.9814583 |
5.8216396 |
-3.401220 |
0.0010863 |
0.2475970 |
FLNC |
| ENSG00000153406 |
0.5476832 |
1.1225174 |
3.392704 |
0.0011159 |
0.2511611 |
NMRAL1 |
| ENSG00000259363 |
0.7834232 |
0.2059661 |
3.382747 |
0.0011515 |
0.2521644 |
ENSG00000259363 |
| ENSG00000261520 |
1.3416498 |
0.5496398 |
3.381676 |
0.0011554 |
0.2521644 |
DLGAP1-AS5 |
| ENSG00000175548 |
-0.5063777 |
4.4022251 |
-3.376397 |
0.0011747 |
0.2521644 |
ALG10B |
| ENSG00000185760 |
1.5278096 |
-0.4446505 |
3.375886 |
0.0011766 |
0.2521644 |
KCNQ5 |
| ENSG00000151834 |
2.3592184 |
-1.6572592 |
3.372175 |
0.0011904 |
0.2521644 |
GABRA2 |
| ENSG00000188107 |
0.4359750 |
3.0692274 |
3.334455 |
0.0013396 |
0.2754604 |
EYS |
| ENSG00000048462 |
-1.2491868 |
-0.2793089 |
-3.333326 |
0.0013444 |
0.2754604 |
TNFRSF17 |
| ENSG00000136842 |
-0.8606898 |
1.1975239 |
-3.332867 |
0.0013463 |
0.2754604 |
TMOD1 |
| ENSG00000170876 |
-0.1548197 |
6.2213758 |
-3.308470 |
0.0014525 |
0.2879399 |
TMEM43 |
| ENSG00000226869 |
1.9505848 |
-1.0381730 |
3.308194 |
0.0014537 |
0.2879399 |
LHFPL3-AS1 |
| ENSG00000185149 |
-1.2408556 |
0.7281455 |
-3.307857 |
0.0014552 |
0.2879399 |
NPY2R |
| ENSG00000203504 |
0.6387076 |
-0.3051535 |
3.299804 |
0.0014921 |
0.2920152 |
ENSG00000203504 |
| ENSG00000187667 |
-0.8113413 |
-0.1035667 |
-3.291976 |
0.0015287 |
0.2959669 |
WHAMMP3 |
Differential expression within each cell type
## Scale for 'x' is already present. Adding another scale for 'x', which
## will replace the existing scale.
## Scale for 'x' is already present. Adding another scale for 'x', which
## will replace the existing scale.

Gene set tests
NPC - roast
| c4.GNF2_CD48 |
20 |
0.2500000 |
0.0000000 |
Down |
0.01 |
0.9826775 |
0.32 |
0.9920713 |
| c5.GO_REGULATION_OF_KERATINOCYTE_PROLIFERATION |
18 |
0.1111111 |
0.2222222 |
Up |
0.01 |
0.9826775 |
0.15 |
0.9920713 |
| decreased_susceptibility_to_type_I_hypersensitivity_reaction |
10 |
0.2000000 |
0.0000000 |
Down |
0.01 |
0.9826775 |
0.19 |
0.9920713 |
| regulation of nitric-oxide synthase activity |
28 |
0.1428571 |
0.0000000 |
Down |
0.01 |
0.9826775 |
0.44 |
0.9920713 |
| regulation of monooxygenase activity |
32 |
0.1250000 |
0.0000000 |
Down |
0.01 |
0.9826775 |
0.63 |
0.9920713 |
| Ligand-gated_ion_channel_transport |
12 |
0.0000000 |
0.5000000 |
Up |
0.02 |
0.9826775 |
0.04 |
0.9920713 |
| c5.GO_GABA_RECEPTOR_ACTIVITY |
11 |
0.0000000 |
0.3636364 |
Up |
0.02 |
0.9826775 |
0.05 |
0.9920713 |
| c2.MOOTHA_GLYCOLYSIS |
17 |
0.2941176 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.11 |
0.9920713 |
| decreased_circulating_tumor_necrosis_factor_level |
25 |
0.2800000 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.12 |
0.9920713 |
| c4.GNF2_VAV1 |
23 |
0.2608696 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.33 |
0.9920713 |
| increased_interleukin-1_beta_secretion |
16 |
0.2500000 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.15 |
0.9920713 |
| c2.LANDEMAINE_LUNG_METASTASIS |
16 |
0.0000000 |
0.2500000 |
Up |
0.02 |
0.9826775 |
0.39 |
0.9920713 |
| c4.GNF2_PAK2 |
22 |
0.2272727 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.17 |
0.9920713 |
| metalloexopeptidase activity |
27 |
0.2222222 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.43 |
0.9920713 |
| c4.GNF2_HLA-C |
33 |
0.2121212 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.33 |
0.9920713 |
| c5.GO_TRANS_GOLGI_NETWORK_TRANSPORT_VESICLE |
27 |
0.1851852 |
0.0740741 |
Down |
0.02 |
0.9826775 |
0.20 |
0.9920713 |
| c2.MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP |
18 |
0.1666667 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.19 |
0.9920713 |
| myosin II complex |
13 |
0.1538462 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.42 |
0.9920713 |
| il8cxcr1_pathway |
20 |
0.1500000 |
0.0000000 |
Down |
0.02 |
0.9826775 |
0.41 |
0.9920713 |
| regulation of interleukin-1 secretion |
9 |
0.0000000 |
0.1111111 |
Up |
0.02 |
0.9826775 |
0.36 |
0.9920713 |
NPC - romer
| c7.GSE29618_LAIV_VS_TIV_FLU_VACCINE_DAY7_MONOCYTE_DN |
157 |
1.01 |
0.01 |
0.01 |
| c7.GSE14413_UNSTIM_VS_IFNB_STIM_NIH3T3_CELLS_UP |
117 |
1.01 |
0.01 |
0.01 |
| increased_susceptibility_to_bacterial_infection |
100 |
1.01 |
0.01 |
0.01 |
| c5.GO_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE |
62 |
1.01 |
0.01 |
0.01 |
| c5.GO_REGULATION_OF_REACTIVE_OXYGEN_SPECIES_BIOSYNTHETIC_PROCESS |
47 |
1.01 |
0.01 |
0.01 |
| negative regulation of inflammatory response |
47 |
1.01 |
0.01 |
0.01 |
| response to type I interferon |
42 |
1.01 |
0.01 |
0.01 |
| c5.GO_RECEPTOR_INTERNALIZATION |
34 |
1.01 |
0.01 |
0.01 |
| abnormal_cellular_extravasation |
21 |
1.01 |
0.01 |
0.01 |
| leukocyte cell-cell adhesion |
18 |
1.01 |
0.01 |
0.01 |
| c2.REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT |
12 |
0.01 |
1.01 |
0.01 |
| Ligand-gated_ion_channel_transport |
12 |
0.01 |
1.01 |
0.01 |
| c5.GO_POSITIVE_REGULATION_OF_LYMPHOCYTE_MIGRATION |
9 |
1.01 |
0.01 |
0.01 |
| abnormal_response_to_infection |
237 |
1.00 |
0.02 |
0.01 |
| c5.GO_RESPONSE_TO_VIRUS |
172 |
1.00 |
0.02 |
0.01 |
| c7.GSE24574_BCL6_HIGH_TFH_VS_TCONV_CD4_TCELL_UP |
160 |
1.00 |
0.02 |
0.01 |
| c7.GSE22432_MULTIPOTENT_PROGENITOR_VS_CDC_UP |
154 |
1.00 |
0.02 |
0.01 |
| c7.GSE7460_FOXP3_MUT_VS_HET_ACT_TCONV_UP |
136 |
1.00 |
0.02 |
0.01 |
| c5.GO_DEFENSE_RESPONSE_TO_VIRUS |
109 |
1.00 |
0.02 |
0.01 |
| defense response to virus |
96 |
1.00 |
0.02 |
0.01 |
Neuron - roast
| c5.GO_DETECTION_OF_CHEMICAL_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION_OF_TASTE |
17 |
0.0000000 |
0.6470588 |
Up |
0.01 |
0.5291039 |
0.01 |
0.7071165 |
| c2.ONO_FOXP3_TARGETS_UP |
15 |
0.4666667 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.10 |
0.7071165 |
| c2.NIKOLSKY_BREAST_CANCER_5P15_AMPLICON |
20 |
0.4000000 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.04 |
0.7071165 |
| c5.GO_REGULATION_OF_INTERLEUKIN_17_PRODUCTION |
8 |
0.3750000 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.03 |
0.7071165 |
| positive regulation of interferon-beta production |
20 |
0.3500000 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.14 |
0.7071165 |
| gws3k-8.6_Red_vs_non-red_hair_color |
15 |
0.3333333 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.02 |
0.7071165 |
| gws3k-8.6_Skin_sensitivity_to_sun |
15 |
0.3333333 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.05 |
0.7071165 |
| abnormal_apical_ectodermal_ridge_morphology |
16 |
0.0625000 |
0.3125000 |
Up |
0.01 |
0.5291039 |
0.15 |
0.7071165 |
| BIOCARTA_TOLL_PATHWAY |
29 |
0.3103448 |
0.0689655 |
Down |
0.01 |
0.5291039 |
0.08 |
0.7071165 |
| regulation of interferon-beta production |
26 |
0.3076923 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.06 |
0.7071165 |
| cone_pathway |
13 |
0.0000000 |
0.3076923 |
Up |
0.01 |
0.5291039 |
0.08 |
0.7071165 |
| c2.PID_CONE_PATHWAY |
13 |
0.0000000 |
0.3076923 |
Up |
0.01 |
0.5291039 |
0.12 |
0.7071165 |
| gws3k-8.6_Serum_albumin_level |
17 |
0.2941176 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.18 |
0.7071165 |
| c5.GO_COP9_SIGNALOSOME |
28 |
0.2857143 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.04 |
0.7071165 |
| receptor internalization |
28 |
0.2857143 |
0.0357143 |
Down |
0.01 |
0.5291039 |
0.09 |
0.7071165 |
| c5.GO_BICELLULAR_TIGHT_JUNCTION_ASSEMBLY |
28 |
0.2857143 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.14 |
0.7071165 |
| positive regulation of interleukin-6 production |
21 |
0.2857143 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.05 |
0.7071165 |
| abnormal_pterygoid_process_morphology |
14 |
0.0714286 |
0.2857143 |
Up |
0.01 |
0.5291039 |
0.03 |
0.7071165 |
| c5.GO_NECROPTOTIC_PROCESS |
14 |
0.2857143 |
0.0000000 |
Down |
0.01 |
0.5291039 |
0.10 |
0.7071165 |
| actin-myosin filament sliding |
18 |
0.2777778 |
0.0555556 |
Down |
0.01 |
0.5291039 |
0.03 |
0.7071165 |
Neuron - romer
| c7.GSE5589_UNSTIM_VS_45MIN_LPS_AND_IL10_STIM_MACROPHAGE_UP |
172 |
1.01 |
0.01 |
0.01 |
| c7.GSE8384_CTRL_VS_B_ABORTUS_4H_MAC_CELL_LINE_DN |
162 |
1.01 |
0.01 |
0.01 |
| c7.GSE17721_CTRL_VS_GARDIQUIMOD_0.5H_BMDC_DN |
159 |
1.01 |
0.01 |
0.01 |
| c7.GSE1925_CTRL_VS_IFNG_PRIMED_MACROPHAGE_24H_IFNG_STIM_UP |
158 |
1.01 |
0.01 |
0.01 |
| c7.GSE21546_WT_VS_ELK1_KO_DP_THYMOCYTES_DN |
151 |
1.01 |
0.01 |
0.01 |
| c7.GSE3039_CD4_TCELL_VS_B1_BCELL_DN |
146 |
1.01 |
0.01 |
0.01 |
| protein complex scaffold |
49 |
1.01 |
0.01 |
0.01 |
| c5.GO_CELLULAR_CARBOHYDRATE_BIOSYNTHETIC_PROCESS |
44 |
1.01 |
0.01 |
0.01 |
| abnormal_temporal_bone_morphology |
30 |
0.01 |
1.01 |
0.01 |
| sensory perception of taste |
26 |
0.01 |
1.01 |
0.01 |
| c2.MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP |
18 |
1.01 |
0.01 |
0.01 |
| abnormal_pterygoid_process_morphology |
14 |
0.01 |
1.01 |
0.01 |
| c5.GO_BITTER_TASTE_RECEPTOR_ACTIVITY |
13 |
0.01 |
1.01 |
0.01 |
| c7.GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN |
177 |
1.00 |
0.02 |
0.01 |
| c7.GSE45365_WT_VS_IFNAR_KO_CD8A_DC_MCMV_INFECTION_UP |
177 |
1.00 |
0.02 |
0.01 |
| negative regulation of cytokine production |
89 |
1.00 |
0.02 |
0.01 |
| c2.KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP |
37 |
1.00 |
0.02 |
0.01 |
| abnormal_chorion_morphology |
33 |
1.00 |
0.02 |
0.01 |
| c5.GO_POSITIVE_REGULATION_OF_INTERFERON_GAMMA_PRODUCTION |
27 |
1.00 |
0.02 |
0.01 |
| c7.GSE3982_CTRL_VS_LPS_1H_NEUTROPHIL_DN |
159 |
0.99 |
0.03 |
0.01 |
Compare logFC between celltypes


Genes with FDR < 30% within NPC or neuron separately
Neuron
| ENSG00000230847 |
-4.1176470 |
-2.0458924 |
-6.121625 |
0.00e+00 |
0.0008056 |
ENSG00000230847 |
| ENSG00000173894 |
0.5551547 |
5.3493957 |
4.617878 |
1.63e-05 |
0.1543658 |
CBX2 |
| ENSG00000115828 |
-1.7332719 |
0.6431161 |
-4.505460 |
2.47e-05 |
0.1560023 |
QPCT |
| ENSG00000164669 |
-1.2307287 |
-0.2461149 |
-4.337493 |
4.56e-05 |
0.2158049 |
INTS4L1 |
| ENSG00000164930 |
-0.7391163 |
4.8643554 |
-4.248241 |
6.29e-05 |
0.2378761 |
FZD6 |
NPC
| ENSG00000230847 |
-3.5818061 |
-2.0458924 |
-5.077991 |
2.80e-06 |
0.0536223 |
ENSG00000230847 |
| ENSG00000226259 |
-1.2943834 |
2.3980778 |
-4.621129 |
1.61e-05 |
0.1046486 |
GTF2H2B |
| ENSG00000164930 |
-0.8172728 |
4.8643554 |
-4.613377 |
1.66e-05 |
0.1046486 |
FZD6 |
| ENSG00000162618 |
-2.3869758 |
-0.7365519 |
-4.429296 |
3.27e-05 |
0.1546567 |
ELTD1 |
| ENSG00000236725 |
-1.1055833 |
0.4658067 |
-4.236436 |
6.56e-05 |
0.2481135 |
ENSG00000236725 |
Effect of correcting for Fibroblast score on case-control t-statistics in NPCs
We have demonstrated that correcting for the fibroblast score is important, especially in boosting concordance with HBCC. So what genes are affected by this correction? In order to test this, I compared the absolute value of the t-statstic (the test-statistic used compute the p-value) from the adjusted and unadjusted test.
| c2.REACTOME_RNA_POL_I_PROMOTER_OPENING |
53 |
3.11 |
22 |
7.07 |
5.205652e-14 |
| c2.REACTOME_AMYLOIDS |
61 |
3.58 |
23 |
6.42 |
1.630978e-13 |
| KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
79 |
4.64 |
26 |
5.60 |
1.805959e-13 |
| c2.KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
80 |
4.70 |
26 |
5.53 |
2.528446e-13 |
| kegg_Systemic_lupus_erythematosus |
80 |
4.70 |
26 |
5.53 |
2.528446e-13 |
| c5.GO_DNA_PACKAGING_COMPLEX |
80 |
4.70 |
25 |
5.32 |
1.977977e-12 |
| c2.REACTOME_PACKAGING_OF_TELOMERE_ENDS |
41 |
2.41 |
18 |
7.48 |
3.281350e-12 |
| KEGG_ALCOHOLISM |
149 |
8.75 |
34 |
3.89 |
5.041777e-12 |
| kegg_Alcoholism |
149 |
8.75 |
34 |
3.89 |
5.041777e-12 |
| CMC-modules_forestgreen |
28 |
1.64 |
15 |
9.12 |
5.556191e-12 |
| c2.REACTOME_RNA_POL_I_TRANSCRIPTION |
78 |
4.58 |
24 |
5.24 |
7.968194e-12 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
9.69 |
35 |
3.61 |
2.248728e-11 |
| c2.REACTOME_MEIOTIC_RECOMBINATION |
71 |
4.17 |
22 |
5.28 |
5.078763e-11 |
| c2.REACTOME_MEIOSIS |
95 |
5.58 |
24 |
4.30 |
7.564072e-10 |
| c2.REACTOME_TELOMERE_MAINTENANCE |
67 |
3.93 |
20 |
5.08 |
8.074538e-10 |
up only
| secondary_FMRP-targets |
770 |
22.64 |
55 |
2.43 |
8.964789e-10 |
| c2.KIM_ALL_DISORDERS_CALB1_CORR_UP |
517 |
15.20 |
42 |
2.76 |
2.518142e-09 |
| CMC-modules_red |
689 |
20.25 |
48 |
2.37 |
2.541420e-08 |
| c5.GO_CELL_PROJECTION |
1508 |
44.33 |
80 |
1.80 |
1.172295e-07 |
| c5.GO_CELL_PROJECTION_PART |
809 |
23.78 |
51 |
2.14 |
2.186483e-07 |
| c5.GO_SYNAPSE |
677 |
19.90 |
45 |
2.26 |
2.751798e-07 |
| kirov_psych.ed.set_mGluR5 |
37 |
1.09 |
9 |
8.27 |
9.066695e-07 |
| kirov_synaptic.sets_mGluR5 |
37 |
1.09 |
9 |
8.27 |
9.066695e-07 |
| primary_mGluR5 |
37 |
1.09 |
9 |
8.27 |
9.066695e-07 |
| c2.WANG_LSD1_TARGETS_DN |
31 |
0.91 |
8 |
8.78 |
2.282486e-06 |
| primary_PSD_(human_core) |
644 |
18.93 |
41 |
2.17 |
2.852382e-06 |
| c5.GO_CYTOSKELETAL_PROTEIN_BINDING |
693 |
20.37 |
43 |
2.11 |
3.130646e-06 |
| cav2_Cav2::ALL |
193 |
5.67 |
19 |
3.35 |
4.282863e-06 |
| c2.BLALOCK_ALZHEIMERS_DISEASE_DN |
1184 |
34.81 |
62 |
1.78 |
5.870449e-06 |
| c4.MODULE_100 |
467 |
13.73 |
32 |
2.33 |
8.398773e-06 |
downonly
| c2.REACTOME_RNA_POL_I_PROMOTER_OPENING |
53 |
1.55 |
22 |
14.15 |
2.321068e-20 |
| c2.REACTOME_AMYLOIDS |
61 |
1.79 |
23 |
12.85 |
4.358139e-20 |
| KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
79 |
2.32 |
25 |
10.79 |
1.461924e-19 |
| c2.KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
80 |
2.35 |
25 |
10.65 |
2.069585e-19 |
| c5.GO_DNA_PACKAGING_COMPLEX |
80 |
2.35 |
25 |
10.65 |
2.069585e-19 |
| kegg_Systemic_lupus_erythematosus |
80 |
2.35 |
25 |
10.65 |
2.069585e-19 |
| c2.REACTOME_RNA_POL_I_TRANSCRIPTION |
78 |
2.29 |
23 |
10.05 |
2.526080e-17 |
| c2.REACTOME_MEIOTIC_RECOMBINATION |
71 |
2.08 |
22 |
10.56 |
3.831306e-17 |
| CMC-modules_forestgreen |
28 |
0.82 |
15 |
18.26 |
2.155808e-16 |
| KEGG_ALCOHOLISM |
149 |
4.37 |
29 |
6.64 |
3.733569e-16 |
| kegg_Alcoholism |
149 |
4.37 |
29 |
6.64 |
3.733569e-16 |
| c5.GO_PROTEIN_DNA_COMPLEX |
141 |
4.14 |
27 |
6.53 |
6.093019e-15 |
| c5.GO_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC |
89 |
2.61 |
22 |
8.43 |
7.612436e-15 |
| c2.REACTOME_PACKAGING_OF_TELOMERE_ENDS |
41 |
1.20 |
16 |
13.30 |
1.218042e-14 |
| c5.GO_CHROMATIN_SILENCING |
73 |
2.14 |
20 |
9.34 |
1.509248e-14 |

Effect of correcting for Fibroblast score on case-control t-statistics in Neurons
| tissue_exp_brain |
495 |
29.13 |
85 |
2.92 |
1.703722e-19 |
| CMC-modules_red |
689 |
40.55 |
89 |
2.19 |
1.306218e-12 |
| c5.GO_SYNAPSE_PART |
549 |
32.31 |
74 |
2.29 |
1.522632e-11 |
| c5.GO_SYNAPSE |
677 |
39.85 |
85 |
2.13 |
1.977615e-11 |
| h.HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
177 |
10.42 |
36 |
3.46 |
4.439413e-11 |
| c5.GO_NEURON_PART |
1088 |
64.04 |
117 |
1.83 |
7.934100e-11 |
| c4.MODULE_47 |
196 |
11.54 |
37 |
3.21 |
2.288108e-10 |
| secondary_FMRP-targets |
770 |
45.32 |
90 |
1.99 |
2.311185e-10 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
9.71 |
33 |
3.40 |
4.544049e-10 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
20.42 |
51 |
2.50 |
1.252737e-09 |
| c5.GO_PRESYNAPTIC_PROCESS_INVOLVED_IN_SYNAPTIC_TRANSMISSION |
101 |
5.94 |
24 |
4.04 |
3.009981e-09 |
| c2.MEISSNER_NPC_HCP_WITH_H3K4ME2 |
390 |
22.95 |
54 |
2.35 |
3.612506e-09 |
| c5.GO_NEURON_PROJECTION |
835 |
49.15 |
91 |
1.85 |
6.490311e-09 |
| abnormal_motor_coordination_balance |
458 |
26.96 |
59 |
2.19 |
1.054544e-08 |
| c5.GO_NEUROTRANSMITTER_TRANSPORT |
133 |
7.83 |
27 |
3.45 |
1.239876e-08 |
up only
| c2.KIM_ALL_DISORDERS_CALB1_CORR_UP |
517 |
15.10 |
46 |
3.05 |
1.583029e-11 |
| CMC-modules_red |
689 |
20.12 |
54 |
2.68 |
3.329240e-11 |
| tissue_exp_brain |
495 |
14.46 |
43 |
2.97 |
1.630936e-10 |
| secondary_FMRP-targets |
770 |
22.49 |
52 |
2.31 |
1.434069e-08 |
| c2.BLALOCK_ALZHEIMERS_DISEASE_DN |
1184 |
34.58 |
68 |
1.97 |
5.070287e-08 |
| c5.GO_SYNAPSE |
677 |
19.77 |
46 |
2.33 |
8.738854e-08 |
| c5.GO_PRESYNAPTIC_PROCESS_INVOLVED_IN_SYNAPTIC_TRANSMISSION |
101 |
2.95 |
15 |
5.09 |
2.271475e-07 |
| c5.GO_SYNAPSE_PART |
549 |
16.03 |
39 |
2.43 |
2.879986e-07 |
| c4.MODULE_100 |
467 |
13.64 |
35 |
2.57 |
3.434816e-07 |
| primary_PSD_(human_core) |
644 |
18.81 |
43 |
2.29 |
3.811836e-07 |
| c4.MODULE_66 |
474 |
13.84 |
35 |
2.53 |
4.881700e-07 |
| kirov_psych.ed.set_mGluR5 |
37 |
1.08 |
9 |
8.33 |
8.584918e-07 |
| kirov_synaptic.sets_mGluR5 |
37 |
1.08 |
9 |
8.33 |
8.584918e-07 |
| primary_mGluR5 |
37 |
1.08 |
9 |
8.33 |
8.584918e-07 |
| c2.REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES |
159 |
4.64 |
18 |
3.88 |
9.357542e-07 |
downonly
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
4.89 |
23 |
4.70 |
6.649058e-10 |
| tissue_exp_brain |
495 |
14.68 |
42 |
2.86 |
8.851474e-10 |
| c2.WONG_ADULT_TISSUE_STEM_MODULE |
591 |
17.52 |
46 |
2.62 |
2.189234e-09 |
| h.HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
177 |
5.25 |
22 |
4.19 |
1.376309e-08 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
10.29 |
31 |
3.01 |
4.817120e-08 |
| c2.SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN |
223 |
6.61 |
24 |
3.63 |
5.156047e-08 |
| c2.CUI_TCF21_TARGETS_2_DN |
744 |
22.06 |
50 |
2.27 |
5.305225e-08 |
| c5.GO_NEURON_PART |
1088 |
32.26 |
64 |
1.98 |
9.817372e-08 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
36.32 |
69 |
1.90 |
1.538746e-07 |
| c5.GO_LEUKOCYTE_MEDIATED_IMMUNITY |
94 |
2.79 |
14 |
5.02 |
6.656525e-07 |
| c5.GO_LYMPHOCYTE_MEDIATED_IMMUNITY |
69 |
2.05 |
12 |
5.86 |
7.622998e-07 |
| c5.GO_CELL_PART_MORPHOGENESIS |
556 |
16.49 |
38 |
2.30 |
1.544832e-06 |
| c5.GO_B_CELL_MEDIATED_IMMUNITY |
40 |
1.19 |
9 |
7.59 |
1.979220e-06 |
| c5.GO_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS |
867 |
25.71 |
51 |
1.98 |
2.241517e-06 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 |
397 |
11.77 |
30 |
2.55 |
2.781861e-06 |

Effective sample size calculations

## Using ID, CellType as id variables
Check Fibroblast signature, NPC and Neurons for CD73 (NT5E) and CD271 (NGFR)

SessionInfo
## R version 3.4.1 (2017-06-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.5 LTS
##
## Matrix products: default
## BLAS/LAPACK: /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid compiler stats4 parallel stats graphics grDevices
## [8] datasets utils methods base
##
## other attached packages:
## [1] sets_1.0-17 VennDiagram_1.6.17
## [3] futile.logger_1.4.3 pheatmap_1.0.8
## [5] GSEABase_1.38.2 graph_1.54.0
## [7] annotate_1.54.0 XML_3.98-1.9
## [9] AnnotationDbi_1.38.2 HTSanalyzeR_2.28.0
## [11] igraph_1.1.2 gage_2.26.1
## [13] GGally_1.3.2 knitr_1.17
## [15] qvalue_2.8.0 reshape2_1.4.2
## [17] xtable_1.8-2 colortools_0.1.5
## [19] preprocessCore_1.38.1 DESeq2_1.16.1
## [21] SummarizedExperiment_1.6.5 DelayedArray_0.2.7
## [23] matrixStats_0.52.2 GenomicRanges_1.28.5
## [25] GenomeInfoDb_1.12.2 IRanges_2.10.3
## [27] S4Vectors_0.14.5 readr_1.1.1
## [29] latex2exp_0.4.0 mixtools_1.1.0
## [31] ape_4.1 ggrepel_0.7.0
## [33] variancePartition_1.6.0 Biobase_2.36.2
## [35] BiocGenerics_0.22.0 ggplot2_2.2.1
## [37] gridExtra_2.3 edgeR_3.18.1
## [39] limma_3.32.7 synapseClient_1.15-0
## [41] doParallel_1.0.11 iterators_1.0.8
## [43] foreach_1.4.3
##
## loaded via a namespace (and not attached):
## [1] backports_1.1.1 Hmisc_4.0-3
## [3] splots_1.42.0 plyr_1.8.4
## [5] lazyeval_0.2.0 splines_3.4.1
## [7] gmp_0.5-13.1 BiocParallel_1.10.1
## [9] digest_0.6.12 BiocInstaller_1.26.1
## [11] htmltools_0.3.6 gdata_2.18.0
## [13] magrittr_1.5 checkmate_1.8.4
## [15] memoise_1.1.0 cluster_2.0.6
## [17] prada_1.52.0 Biostrings_2.44.2
## [19] colorspace_1.3-2 blob_1.1.0
## [21] rrcov_1.4-3 RCurl_1.95-4.8
## [23] genefilter_1.58.1 lme4_1.1-14
## [25] survival_2.41-3 gtable_0.2.0
## [27] zlibbioc_1.22.0 XVector_0.16.0
## [29] RankProd_3.2.0 Rmpfr_0.6-1
## [31] cellHTS2_2.40.0 DEoptimR_1.0-8
## [33] scales_0.5.0 futile.options_1.0.0
## [35] vsn_3.44.0 mvtnorm_1.0-6
## [37] DBI_0.7 Rcpp_0.12.13
## [39] htmlTable_1.9 foreign_0.8-69
## [41] bit_1.1-12 Formula_1.2-2
## [43] htmlwidgets_0.9 httr_1.3.1
## [45] gplots_3.0.1 RColorBrewer_1.1-2
## [47] acepack_1.4.1 pkgconfig_2.0.1
## [49] reshape_0.8.7 nnet_7.3-12
## [51] locfit_1.5-9.1 labeling_0.3
## [53] rlang_0.1.2 munsell_0.4.3
## [55] tools_3.4.1 RSQLite_2.0
## [57] evaluate_0.10.1 stringr_1.2.0
## [59] yaml_2.1.14 bit64_0.9-7
## [61] robustbase_0.92-7 caTools_1.17.1
## [63] KEGGREST_1.16.1 RBGL_1.52.0
## [65] nlme_3.1-131 BioNet_1.36.0
## [67] biomaRt_2.32.1 pbkrtest_0.4-7
## [69] png_0.1-7 affyio_1.46.0
## [71] statmod_1.4.30 tibble_1.3.4
## [73] geneplotter_1.54.0 pcaPP_1.9-72
## [75] stringi_1.1.5 highr_0.6
## [77] lattice_0.20-35 Matrix_1.2-11
## [79] nloptr_1.0.4 data.table_1.10.4
## [81] bitops_1.0-6 colorRamps_2.3
## [83] R6_2.2.2 latticeExtra_0.6-28
## [85] affy_1.54.0 hwriter_1.3.2
## [87] KernSmooth_2.23-15 codetools_0.2-15
## [89] lambda.r_1.2 MASS_7.3-47
## [91] gtools_3.5.0 Category_2.42.1
## [93] rprojroot_1.2 rjson_0.2.15
## [95] GenomeInfoDbData_0.99.0 hms_0.3
## [97] rpart_4.1-11 minqa_1.2.4
## [99] rmarkdown_1.6 segmented_0.5-2.2
## [101] base64enc_0.1-3